He was the son of Col. Richard Lee II, Esq., "the Scholar" (1647-1715) and Laetitia Corbin (ca. 1657-1706). Born at Machodoc in Westmoreland County, Lee resided at Lee Hall near Hague, in the Parish of Cople, Westmoreland County. All traces of the house have long since disappeared. The land surrounding Lee Hall was part of the of Machodoc land patented in 1650 by his grandfather, Col. Richard Lee I, Esq., “the Immigrant” (1618-1664). Henry died between June 13–25, 1747.

He was a co-leaseholder with his brother Thomas of the family plantation on the Machodoc River, and he owned or leased the area of Lee Hall. When the family plantation was burned down in January 1729, Henry Lee took in his brother's family at Lee Hall while the plantation was rebuilt.